Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtccttgtatgttgtagtcttgctttgaccttgatatagaaggttcagaagatatgctgttttgagttttgtcatatttatctgattttgttgtattcatttgtcataaattatgcagCGAATAACAATCCCTGAAATCCGGAATCATAGTTGGTTCCTGAAGAACCTTCCTGCTGATCTGATGGATGATGATAGCATGAGCAACCAATATGAGGAGC

Basic information

species Zea mays
transcript GRMZM2G138861_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G138861_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os03g55600.1 (Oryza sativa), 3'ss of exon 8
gtaagtccttgtatgttgtagtcttgctttgaccttgatatagaaggt--tcagaagatatgctgttttgagttttgtcatatttatctgattttgttgtattcatttgtcataaattatgcagCGAATAACAATCCCTGAAATCCGGAATCATAGTTGGTTCCTGAAGAACCTTCCTGCTGATCTGATGGATGATGATAGCATGAGCAACCAATATGAGGAGC
                  |  | |   |||    ||||| ||   | |  ||     | ||||  ||   | |||||  | |||      |||||  ||      ||  | ||     |||||| | ||||||||||| ||||| ||||  ||| | |||||| |||||||||||||||| ||| ||||||| |||||||| ||||||| ||| |||||||| |
------------------ttatttgtgtttatagttgatgtaattgttaatcgttgtaaatgcatttcaaaattttggtacatt------attttcatgacacttttgatgatggcaaatgcagAGGATAACAATCCCAGAAATACGGAGCCATGGCTGGTTCTTGAAGAACCTTCCTGCAGATTTGATGGACGATGATAGTATGAGCAGCCAGTATGAGGAAC
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|60341330|gb|DN208303.1|DN208303
EST:     CAGAGTGCAGGCATCTAATTTCGAGGATTTTTGTTGGCGATCCTGCTACG                         CGAATAACAATCCCTGAAATCCGGAATCATAGTTGGTTCCTGAAGAACCTT
genomic: CAGAGTGCAGGCATCTAATTTCGAGGATTTTTGTTGGCGATCCTGCTACGgtaagtcctt ... aattatgcagCGAATAACAATCCCTGAAATCCGGAATCATAGTTGGTTCCTGAAGAACCTT
EST: gi|211499758|gb|FL295246.1|FL295246
EST:     CAGAGTGCAGGCATCTAATTTCGAGGATTTTTGTTGGCGATCCTGCTACG                         CGAATAACAATCCCTGAAATCCGGAATCATAGTTGGTTCCTGAAGAACCTT
genomic: CAGAGTGCAGGCATCTAATTTCGAGGATTTTTGTTGGCGATCCTGCTACGgtaagtcctt ... aattatgcagCGAATAACAATCCCTGAAATCCGGAATCATAGTTGGTTCCTGAAGAACCTT
EST: gi|60348192|gb|DN215165.1|DN215165
EST:     CAGAGTGCAGGCATCTAATTTCGAGGATTTTTGTTGGCGATCCTGCTACG                         CGAATAACAATCCCTGAAATCCGGAATCATAGTTGGTTCCTGAAGAACCTT
genomic: CAGAGTGCAGGCATCTAATTTCGAGGATTTTTGTTGGCGATCCTGCTACGgtaagtcctt ... aattatgcagCGAATAACAATCCCTGAAATCCGGAATCATAGTTGGTTCCTGAAGAACCTT
EST: gi|6095661|gb|AW120328.1|AW120328
EST:     CAGAGTGCAGGCATCTAATTTCGAGGATTTTTGTTGGCGATCCTGCTACG                         CGAATAACAATCCCTGAAATCCGGAATCATAGTTGGTTCCTGAAGAACCTT
genomic: CAGAGTGCAGGCATCTAATTTCGAGGATTTTTGTTGGCGATCCTGCTACGgtaagtcctt ... aattatgcagCGAATAACAATCCCTGAAATCCGGAATCATAGTTGGTTCCTGAAGAACCTT
EST: gi|211499755|gb|FL295243.1|FL295243
EST:     CAGAGTGCAGGCATCTAATTTCGAGGATTTTTGTTGGCGATCCTGCTACG                         CGAATAACAATCCCTGAAATCCGGAATCATAGTTGGTTCCTGAAGAACCTT
genomic: CAGAGTGCAGGCATCTAATTTCGAGGATTTTTGTTGGCGATCCTGCTACGgtaagtcctt ... aattatgcagCGAATAACAATCCCTGAAATCCGGAATCATAGTTGGTTCCTGAAGAACCTT
EST: gi|78111738|gb|DV530135.1|DV530135
EST:     CAGAGTGCAGGCATCTAATTTCGAGGATTTTTGTTGGCGATCCTGCTACG                         CGAATAACAATCCCTGAAATCCGGAATCATAGTTGGTTCCTGAAGAACCTT
genomic: CAGAGTGCAGGCATCTAATTTCGAGGATTTTTGTTGGCGATCCTGCTACGgtaagtcctt ... aattatgcagCGAATAACAATCCCTGAAATCCGGAATCATAGTTGGTTCCTGAAGAACCTT
EST: gi|6194772|gb|AW146876.1|AW146876
EST:     CAGAGTGCAGGCATCTAATTTCGAGGATTTTTGTTGGCGATCCTGCTACG                         CGAATAACAATCCCTGAAATCCGGAATCATAGTTGGTTCCTGAAGAACCTT
genomic: CAGAGTGCAGGCATCTAATTTCGAGGATTTTTGTTGGCGATCCTGCTACGgtaagtcctt ... aattatgcagCGAATAACAATCCCTGAAATCCGGAATCATAGTTGGTTCCTGAAGAACCTT
EST: gi|148948002|gb|EC893502.2|EC893502
EST:     CAGAGTGCAGGCATCTAATTTCGAGGATTTTTGTTGGCGATCCTGCTACG                         CGAATAACAATCCCTGAAATCCGGAATCATAGTTGGTTCCTGAAGAACCTT
genomic: CAGAGTGCAGGCATCTAATTTCGAGGATTTTTGTTGGCGATCCTGCTACGgtaagtcctt ... aattatgcagCGAATAACAATCCCTGAAATCCGGAATCATAGTTGGTTCCTGAAGAACCTT
EST: gi|149009071|gb|EE153785.2|EE153785
EST:     CAGAGTGCAGGCATCTAATTTCGAGGATTTTTGTTGGCGATCCTGCTACG                         CGAATAACAATCCCTGAAATCCGGAATCATAGTTGGTTCCTGAAGAACCTT
genomic: CAGAGTGCAGGCATCTAATTTCGAGGATTTTTGTTGGCGATCCTGCTACGgtaagtcctt ... aattatgcagCGAATAACAATCCCTGAAATCCGGAATCATAGTTGGTTCCTGAAGAACCTT
EST: gi|30087423|gb|CB885629.1|CB885629
EST:     CAGAGTGCAGGCATCTAATTTCGAGGATTTTTGTTGGCGATCCTGCTACG                         CGAATAACAATCCCTGAAATCCGGAATCATAGTTGGTTCCTGAAGAACCTT
genomic: CAGAGTGCAGGCATCTAATTTCGAGGATTTTTGTTGGCGATCCTGCTACGgtaagtcctt ... aattatgcagCGAATAACAATCCCTGAAATCCGGAATCATAGTTGGTTCCTGAAGAACCTT
EST: gi|31357636|gb|CD441993.1|CD441993
EST:     CAGAGTGCAGGCATCTAATTTCGAGGATTTTTGTTGGCGATCCTGCTACG                         CGAATAACAATCCCTGAAATCCGGAATCATAGTTGGTTCCTGAAGAACCTT
genomic: CAGAGTGCAGGCATCTAATTTCGAGGATTTTTGTTGGCGATCCTGCTACGgtaagtcctt ... aattatgcagCGAATAACAATCCCTGAAATCCGGAATCATAGTTGGTTCCTGAAGAACCTT
EST: gi|31362713|gb|CD447070.1|CD447070
EST:     CAGAGTGCAGGCATCTAATTTCGAGGATTTTTGTTGGCGATCCTGCTACG                         CGAATAACAATCCCTGAAATCCGGAATCATAGTTGGTTCCTGAAGAACCTT
genomic: CAGAGTGCAGGCATCTAATTTCGAGGATTTTTGTTGGCGATCCTGCTACGgtaagtcctt ... aattatgcagCGAATAACAATCCCTGAAATCCGGAATCATAGTTGGTTCCTGAAGAACCTT
EST: gi|149103213|gb|EE288586.2|EE288586
EST:     CAGAGTGCAGGCATCTAATTTCGAGGATTTTTGTTGGCGATCCTGCTACG                         CGAATAACAATCCCTGAAATCCGGAATCATAGTTGGTTCCTGAAGAACCTT
genomic: CAGAGTGCAGGCATCTAATTTCGAGGATTTTTGTTGGCGATCCTGCTACGgtaagtcctt ... aattatgcagCGAATAACAATCCCTGAAATCCGGAATCATAGTTGGTTCCTGAAGAACCTT
EST: gi|33092236|gb|CF052230.1|CF052230
EST:     CAGAGTGCAGGCATCTAATTTCGAGGATTTTTGTTGGCGATCCTGCTACG                         CGAATAACAATCCCTGAAATCCGGAATCATAGTTGGGTTCCTGAAGAACCT
genomic: CAGAGTGCAGGCATCTAATTTCGAGGATTTTTGTTGGCGATCCTGCTACGgtaagtcctt ... aattatgcagCGAATAACAATCCCTGAAATCCGGAATCATAGTT-GGTTCCTGAAGAACCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagttttgtcatatttatctgattttgttgtattcatttgtcataaattatgcagCGAATAACAATCCCTGAAATCCGGAATCATAGTTGGTTCCTGAAGAACCTTCCTGCTGATCTGATGGATGATGATAGCATGAGCAACCAATATGAGGAGC
                atctgat  putative branch site (score: 4)
                              tattcatttgtcataa  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtccttgtatgttgtagtcttgctttgaccttgatatagaaggttcagaagatatgctgttttgagttttgtcatatttatctgattttgttgtattcatttgtcataaattatgcagCGAATAACAATCCCTGAAATCCGGAATCATAGTTGGTTCCTGAAGAACCTTCCTGCTGATCTGATGGATGATGATAGCATGAGCAACCAATATGAGGAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG